Mass: 1995.093 Da / Num. of mol.: 8 / Source method: obtained synthetically Details: The RNA hexamer UGAGGU where the 2nd G was replaced by a C8-brominated Gd was phased using radiation damage on the highly susceptible Br-C8 bond.
Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.77 Å3/Da / Density % sol: 30.64 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR ...Details: 1 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution: 1.4→1.48 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3438 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 20 Å / Redundancy: 4.2 %
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 98.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.1
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Processing
Software
Name
Version
Classification
ProDC
datacollection
XDS
datareduction
SHELXD
phasing
SHARP
phasing
REFMAC
5.1.24
refinement
XDS
datascaling
Refinement
Method to determine structure: RIP - Radiation-damage Induced Phasing Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 0.986 / SU ML: 0.039 Isotropic thermal model: The DNA/RNA and K-atoms were refined anisotropically, the spermine and waters isotropic Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.071 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The model was built and refined against the data set collected before the "X-ray burn". Afterwards, the model was refined for some additional cycles against the data set that was collected ...Details: The model was built and refined against the data set collected before the "X-ray burn". Afterwards, the model was refined for some additional cycles against the data set that was collected after the "X-ray burn". No manual adjustments were made, resulting in strong negative densities in the Fo-Fc difference map on X-ray susceptible sites, such as the Br-atoms.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19949
1148
5 %
RANDOM
Rwork
0.15216
-
-
-
all
0.15453
22939
-
-
obs
0.15453
22939
99.44 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 9.645 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.24 Å2
0 Å2
0 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0.25 Å2
Refinement step
Cycle: LAST / Resolution: 1.4→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
1024
31
181
1236
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.021
1171
X-RAY DIFFRACTION
r_angle_refined_deg
1.935
3
1778
X-RAY DIFFRACTION
r_chiral_restr
0.108
0.2
184
X-RAY DIFFRACTION
r_gen_planes_refined
0.021
0.02
520
X-RAY DIFFRACTION
r_nbd_refined
0.412
0.2
409
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.119
0.2
139
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.138
0.2
35
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.185
0.2
22
X-RAY DIFFRACTION
r_scbond_it
3.131
3
1164
X-RAY DIFFRACTION
r_scangle_it
3.844
4.5
1778
X-RAY DIFFRACTION
r_rigid_bond_restr
2.128
2
1144
X-RAY DIFFRACTION
r_sphericity_free
4.347
5
17
X-RAY DIFFRACTION
r_sphericity_bonded
5.791
5
1016
LS refinement shell
Resolution: 1.4→1.476 Å / Total num. of bins used: 10 /
Rfactor
Num. reflection
Rfree
0.286
155
Rwork
0.194
3104
Refinement
*PLUS
Highest resolution: 1.42 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.48 Å
+
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